C++ wrapper of HDF5 library based on HighFive project. It also includes python bindings h5gtpy that you can install with cmake.

h5gtpy doesn't provide pip install as it is inteded to be used only for projects that run on both C++ and python sides.

h5gtpy uses pybind11 to make python bindings and there may be some perfomance penalty when copying matrices from C++ Eigen3 matrices to numpy (or std::vector to py::list). No perfomance testing were done.

This project is aimed at developers who uses C++ along with python. If you only need python HDF5 API you should better refer to h5py project. That is why h5gtpy doesn't provide pip install

Documentation

Common documentation: h5gt.readthedocs.io

C++ API documentation: tierra-colada.github.io/h5gt

Building h5gt

As h5gt is header only library you don't need to buid it (but of course you can do that). See src/examples and tests/unit for usage examples.

Building h5gtpy

To build with python support you need:

• set H5GT_BUILD_h5gtpy to ON
• provide python to cmake (I do it with PYTHON_EXECUTABLE=/path/to/python.exe)
• enable Eigen3 support H5GT_USE_EIGEN=ON (Eigen3_ROOT is enough to find eigen)
• specify HDF5_RUNTIME_DIRS containing HDF5-runtime (probably it is enough to have it in PATH env)
• build HDF5 as SHARED C library

i.e. configure it with:

mkdir build
cd build
cmake .. 
  -DH5GT_BUILD_h5gtpy=ON 
  -DPYTHON_EXECUTABLE=/path/to/python.exe 
  -DH5GT_USE_EIGEN=ON 
  -DEigen3_ROOT=/path/to/eigen3 
  -DHDF5_DIR=/path/to/hdf5-config.cmake 
  -DHDF5_RUNTIME_DIRS=/path/to/hdf5-runtime   
  -DZLIB_RUNTIME_DIRS=/path/to/zlib-runtime
  -DH5GTPY_COPY_RUNTIME_DEPS=OFF
cmake --build . 

If your HDF5 depends on ZLIB or MPI you may also need to add it.

To run h5gtpy python must know where HDF5-runtime is. You may choose whether to copy HDF5-runtime to site-packages/h5gtpy dir or add this dir to path env (done automatically at installation step when H5GTPY_COPY_RUNTIME_DEPS=OFF).

Installation h5gtpy

h5gtpy installation is done the same way one usually installs cmake project:

cmake --install . --prefix /some/path --config Release`

Then you can find h5gtpy in site-packages of your python env.

NOTE: cmake tries to find runtime dependencies at install step. If there are unresolved or conflict dependencies then you need to modify PATH env, rerun cmake .. and cmake --install . --prefix /some/path --config Release. You don't have to rebuild the project!

Usage

Importing is done via:

from h5gtpy import h5gt

A test is also given in site-packages/h5gtpy. To run test:

python -m unittest discover h5gtpy.tests

Integrating with VS Code

There is stub file h5gtpy/h5gt.pyi. You need to set VS Code setting "python.analysis.stubPath": "some/relative/path/to/stub-storage": where stub-storage is supposed to contain folder h5gtpy with h5gt.pyi file.

I'm some kind of a uncomfortable to distribute stub file, so to be sure that stub file is updated you can generate your own stub file:

pip install pybind11-stubgen
pybind11-stubgen --no-setup-py h5gtpy._h5gt

Integrating with PyCharm

You don't need to provide stub file to PyCharm as it handles this by its own.

Supported HDF5 versions

1.10, 1.12 (recommended)

Supported platforms

Windows 10, Linux, OSX